I am aware of chests emptying when you upgrade/downgrade. I don't think this is the same problem because chests in unloaded chunks weren't affected. Hence why I only lost my inventory in the recent upgrade/downgrade glitch, not any of my stuff back at home base. These minecart chests should similarly have been unaffected.

Anyway, I am exploring a new abandoned mineshaft. I might just have been very unlucky, but all four of the minecarts with chests I have found so far have been completely empty. Theoretically possible, but it stretches probability. The chunks affected were spawned many weeks ago, but I have only been in the actual mineshafts since upgrading to 14w18b.